Report insertions stripped during alignment #449
Merged
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Motivated by a comment in today's lab meeting this PR reports insertions in
augur align
which are removed as we (typically) strip to reference.It (a) prints them to screen and (b) produces a CSV you can drag&drop onto auspice to view the insertions. Numbering is GFF style -- 1 based, insertion to the right.
E.g. here's (some) of the output from a zika run:
and via the auspice visualisation:
If we like this direction, there's lots more we can do here, for instance cross reference with the (genbank) reference to see what genes they fall in, translate the insertions if they look like codon insertions etc etc.